1
|
Bradley CC, Wang C, Gordon AJE, Wen AX, Luna PN, Cooke MB, Kohrn BF, Kennedy SR, Avadhanula V, Piedra PA, Lichtarge O, Shaw CA, Ronca SE, Herman C. Targeted accurate RNA consensus sequencing (tARC-seq) reveals mechanisms of replication error affecting SARS-CoV-2 divergence. Nat Microbiol 2024; 9:1382-1392. [PMID: 38649410 DOI: 10.1038/s41564-024-01655-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 02/28/2024] [Indexed: 04/25/2024]
Abstract
RNA viruses, like SARS-CoV-2, depend on their RNA-dependent RNA polymerases (RdRp) for replication, which is error prone. Monitoring replication errors is crucial for understanding the virus's evolution. Current methods lack the precision to detect rare de novo RNA mutations, particularly in low-input samples such as those from patients. Here we introduce a targeted accurate RNA consensus sequencing method (tARC-seq) to accurately determine the mutation frequency and types in SARS-CoV-2, both in cell culture and clinical samples. Our findings show an average of 2.68 × 10-5 de novo errors per cycle with a C > T bias that cannot be solely attributed to APOBEC editing. We identified hotspots and cold spots throughout the genome, correlating with high or low GC content, and pinpointed transcription regulatory sites as regions more susceptible to errors. tARC-seq captured template switching events including insertions, deletions and complex mutations. These insights shed light on the genetic diversity generation and evolutionary dynamics of SARS-CoV-2.
Collapse
Affiliation(s)
- Catherine C Bradley
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor College of Medicine Medical Scientist Training Program, Houston, TX, USA
- Robert and Janice McNair Foundation/ McNair Medical Institute M.D./Ph.D. Scholars program, Houston, TX, USA
| | - Chen Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Alasdair J E Gordon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Alice X Wen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor College of Medicine Medical Scientist Training Program, Houston, TX, USA
- Robert and Janice McNair Foundation/ McNair Medical Institute M.D./Ph.D. Scholars program, Houston, TX, USA
| | - Pamela N Luna
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Matthew B Cooke
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Brendan F Kohrn
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Scott R Kennedy
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Vasanthi Avadhanula
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Pedro A Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Olivier Lichtarge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Chad A Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Shannon E Ronca
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Feigin Biosafety Level 3 Facility, Texas Children's Hospital, Houston, TX, USA
- National School of Tropical Medicine, Department of Pediatrics Tropical Medicine, Texas Children's Hospital and Baylor College of Medicine, Houston, TX, USA
| | - Christophe Herman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA.
| |
Collapse
|
2
|
Kunisetty B, Martin-Giacalone BA, Zhao X, Luna PN, Brooks BP, Hufnagel RB, Shaw CA, Rosenfeld JA, Agopian AJ, Lupo PJ, Scott DA. High Clinical Exome Sequencing Diagnostic Rates and Novel Phenotypic Expansions for Nonisolated Microphthalmia, Anophthalmia, and Coloboma. Invest Ophthalmol Vis Sci 2024; 65:25. [PMID: 38502138 PMCID: PMC10959191 DOI: 10.1167/iovs.65.3.25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 02/26/2024] [Indexed: 03/20/2024] Open
Abstract
Purpose A molecular diagnosis is only made in a subset of individuals with nonisolated microphthalmia, anophthalmia, and coloboma (MAC). This may be due to underutilization of clinical (whole) exome sequencing (cES) and an incomplete understanding of the genes that cause MAC. The purpose of this study is to determine the efficacy of cES in cases of nonisolated MAC and to identify new MAC phenotypic expansions. Methods We determined the efficacy of cES in 189 individuals with nonisolated MAC. We then used cES data, a validated machine learning algorithm, and previously published expression data, case reports, and animal models to determine which candidate genes were most likely to contribute to the development of MAC. Results We found the efficacy of cES in nonisolated MAC to be between 32.3% (61/189) and 48.1% (91/189). Most genes affected in our cohort were not among genes currently screened in clinically available ophthalmologic gene panels. A subset of the genes implicated in our cohort had not been clearly associated with MAC. Our analyses revealed sufficient evidence to support low-penetrance MAC phenotypic expansions involving nine of these human disease genes. Conclusions We conclude that cES is an effective means of identifying a molecular diagnosis in individuals with nonisolated MAC and may identify putatively damaging variants that would be missed if only a clinically available ophthalmologic gene panel was obtained. Our data also suggest that deleterious variants in BRCA2, BRIP1, KAT6A, KAT6B, NSF, RAC1, SMARCA4, SMC1A, and TUBA1A can contribute to the development of MAC.
Collapse
Affiliation(s)
- Bhavana Kunisetty
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
| | - Bailey A. Martin-Giacalone
- Division of Public Health Sciences, Department of Surgery, Washington University School of Medicine, St. Louis, Missouri, United States
- Section of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, United States
| | - Xiaonan Zhao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
- Baylor Genetics, Houston, Texas, United States
| | - Pamela N. Luna
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
| | - Brian P. Brooks
- Ophthalmic Genetics & Visual Function Branch, National Eye Institute, NIH, Bethesda, Maryland, United States
| | - Robert B. Hufnagel
- Ophthalmic Genetics & Visual Function Branch, National Eye Institute, NIH, Bethesda, Maryland, United States
| | - Chad A. Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
| | - Jill A. Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
| | - A. J. Agopian
- Department of Epidemiology, Human Genetics & Environmental Sciences, UTHealth School of Public Health, Houston, Texas, United States
| | - Philip J. Lupo
- Section of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, United States
| | - Daryl A. Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas, United States
| |
Collapse
|
3
|
Huth EA, Zhao X, Owen N, Luna PN, Vogel I, Dorf ILH, Joss S, Clayton-Smith J, Parker MJ, Louw JJ, Gewillig M, Breckpot J, Kraus A, Sasaki E, Kini U, Burgess T, Tan TY, Armstrong R, Neas K, Ferrero GB, Brusco A, Kerstjens-Frederikse WS, Rankin J, Helvaty LR, Landis BJ, Geddes GC, McBride KL, Ware SM, Shaw CA, Lalani SR, Rosenfeld JA, Scott DA. Clinical exome sequencing efficacy and phenotypic expansions involving anomalous pulmonary venous return. Eur J Hum Genet 2023; 31:1430-1439. [PMID: 37673932 PMCID: PMC10689790 DOI: 10.1038/s41431-023-01451-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 08/08/2023] [Accepted: 08/24/2023] [Indexed: 09/08/2023] Open
Abstract
Anomalous pulmonary venous return (APVR) frequently occurs with other congenital heart defects (CHDs) or extra-cardiac anomalies. While some genetic causes have been identified, the optimal approach to genetic testing in individuals with APVR remains uncertain, and the etiology of most cases of APVR is unclear. Here, we analyzed molecular data from 49 individuals to determine the diagnostic yield of clinical exome sequencing (ES) for non-isolated APVR. A definitive or probable diagnosis was made for 8 of those individuals yielding a diagnostic efficacy rate of 16.3%. We then analyzed molecular data from 62 individuals with APVR accrued from three databases to identify novel APVR genes. Based on data from this analysis, published case reports, mouse models, and/or similarity to known APVR genes as revealed by a machine learning algorithm, we identified 3 genes-EFTUD2, NAA15, and NKX2-1-for which there is sufficient evidence to support phenotypic expansion to include APVR. We also provide evidence that 3 recurrent copy number variants contribute to the development of APVR: proximal 1q21.1 microdeletions involving RBM8A and PDZK1, recurrent BP1-BP2 15q11.2 deletions, and central 22q11.2 deletions involving CRKL. Our results suggest that ES and chromosomal microarray analysis (or genome sequencing) should be considered for individuals with non-isolated APVR for whom a genetic etiology has not been identified, and that genetic testing to identify an independent genetic etiology of APVR is not warranted in individuals with EFTUD2-, NAA15-, and NKX2-1-related disorders.
Collapse
Affiliation(s)
- Emily A Huth
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Xiaonan Zhao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Baylor Genetics, Houston, TX, USA
| | - Nichole Owen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Baylor Genetics, Houston, TX, USA
| | - Pamela N Luna
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ida Vogel
- Department of Clinical Medicine, Aarhus University, 8000, Aarhus, C, Denmark
| | - Inger L H Dorf
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | - Shelagh Joss
- West of Scotland Genomics Service, Queen Elizabeth University Hospital, Glasgow, G51 4TF, UK
| | - Jill Clayton-Smith
- Manchester Centre For Genomic Medicine, Manchester University Hospitals, Manchester, M13 9WL, UK
- University of Manchester, Manchester, M13 9PL, UK
| | - Michael J Parker
- Department of Clinical Genetics, Sheffield, Children's Hospital, UK
| | - Jacoba J Louw
- Pediatric Cardiology Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Marc Gewillig
- Department of Cardiovascular Sciences KU Leuven, Leuven, Belgium
- Pediatric Cardiology University Hospitals Leuven, Leuven, Belgium
| | - Jeroen Breckpot
- Center for Human Genetics, University Hospitals Leuven, Catholic University, Leuven, Belgium
| | - Alison Kraus
- Yorkshire Regional Genetics Service, Chapel Allerton Hospital, Leeds, LS7 4SA, UK
| | - Erina Sasaki
- Oxford Centre for Genomic Medicine, Oxford University Hospital, Oxford, OX3 7HE, UK
| | - Usha Kini
- Oxford Centre for Genomic Medicine, Oxford University Hospital, Oxford, OX3 7HE, UK
- Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DU, UK
| | - Trent Burgess
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Tiong Y Tan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Ruth Armstrong
- East Anglian Medical Genetics Service, Addenbrooke's Treatment Centre, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK
| | | | - Giovanni B Ferrero
- Department of Clinical and Biological Sciences, University of Torino, Orbassano, Italy
| | - Alfredo Brusco
- Department of Medical Sciences, University of Torino, Torino, Italy
- Città della Salute e della Scienza University Hospital, Torino, Italy
| | | | | | | | | | - Gabrielle C Geddes
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Kim L McBride
- Department of Medical Genetics, University of Calgary, Calgary, Alberta, Canada
- Center for Cardiovascular Research, Nationwide Children's Hospital, Columbus, OH, USA
| | - Stephanie M Ware
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Chad A Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Seema R Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Daryl A Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA.
| |
Collapse
|
4
|
Zhang X, Irajizad E, Hoffman KL, Fahrmann JF, Li F, Seo YD, Browman GJ, Dennison JB, Vykoukal J, Luna PN, Siu W, Wu R, Murage E, Ajami NJ, McQuade JL, Wargo JA, Long JP, Do KA, Lampe JW, Basen-Engquist KM, Okhuysen PC, Kopetz S, Hanash SM, Petrosino JF, Scheet P, Daniel CR. Modulating a prebiotic food source influences inflammation and immune-regulating gut microbes and metabolites: insights from the BE GONE trial. EBioMedicine 2023; 98:104873. [PMID: 38040541 PMCID: PMC10755114 DOI: 10.1016/j.ebiom.2023.104873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 10/06/2023] [Accepted: 10/31/2023] [Indexed: 12/03/2023] Open
Abstract
BACKGROUND Accessible prebiotic foods hold strong potential to jointly target gut health and metabolic health in high-risk patients. The BE GONE trial targeted the gut microbiota of obese surveillance patients with a history of colorectal neoplasia through a straightforward bean intervention. METHODS This low-risk, non-invasive dietary intervention trial was conducted at MD Anderson Cancer Center (Houston, TX, USA). Following a 4-week equilibration, patients were randomized to continue their usual diet without beans (control) or to add a daily cup of study beans to their usual diet (intervention) with immediate crossover at 8-weeks. Stool and fasting blood were collected every 4 weeks to assess the primary outcome of intra and inter-individual changes in the gut microbiome and in circulating markers and metabolites within 8 weeks. This study was registered on ClinicalTrials.gov as NCT02843425, recruitment is complete and long-term follow-up continues. FINDINGS Of the 55 patients randomized by intervention sequence, 87% completed the 16-week trial, demonstrating an increase on-intervention in diversity [n = 48; linear mixed effect and 95% CI for inverse Simpson index: 0.16 (0.02, 0.30); p = 0.02] and shifts in multiple bacteria indicative of prebiotic efficacy, including increased Faecalibacterium, Eubacterium and Bifidobacterium (all p < 0.05). The circulating metabolome showed parallel shifts in nutrient and microbiome-derived metabolites, including increased pipecolic acid and decreased indole (all p < 0.002) that regressed upon returning to the usual diet. No significant changes were observed in circulating lipoproteins within 8 weeks; however, proteomic biomarkers of intestinal and systemic inflammatory response, fibroblast-growth factor-19 increased, and interleukin-10 receptor-α decreased (p = 0.01). INTERPRETATION These findings underscore the prebiotic and potential therapeutic role of beans to enhance the gut microbiome and to regulate host markers associated with metabolic obesity and colorectal cancer, while further emphasizing the need for consistent and sustainable dietary adjustments in high-risk patients. FUNDING This study was funded by the American Cancer Society.
Collapse
Affiliation(s)
- Xiaotao Zhang
- Division of Cancer Prevention and Population Sciences, Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Institute for Translational Epidemiology & Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ehsan Irajizad
- Division of Basic Sciences, Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kristi L Hoffman
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Johannes F Fahrmann
- Red & Charline McCombs Institute for the Early Detection and Treatment of Cancer, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Division of Cancer Prevention and Population Sciences, Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Fangyu Li
- Division of Cancer Prevention and Population Sciences, Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yongwoo David Seo
- Division of Surgery, Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Gladys J Browman
- Division of Cancer Prevention and Population Sciences, Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jennifer B Dennison
- Red & Charline McCombs Institute for the Early Detection and Treatment of Cancer, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jody Vykoukal
- Red & Charline McCombs Institute for the Early Detection and Treatment of Cancer, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Pamela N Luna
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Wesley Siu
- Division of Cancer Prevention and Population Sciences, Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ranran Wu
- Red & Charline McCombs Institute for the Early Detection and Treatment of Cancer, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Eunice Murage
- Red & Charline McCombs Institute for the Early Detection and Treatment of Cancer, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Nadim J Ajami
- Platform for Innovative Microbiome and Translational Research, Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jennifer L McQuade
- Division of Cancer Medicine, Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jennifer A Wargo
- Division of Surgery, Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Platform for Innovative Microbiome and Translational Research, Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - James P Long
- Division of Basic Sciences, Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kim-Anh Do
- Division of Basic Sciences, Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Johanna W Lampe
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Karen M Basen-Engquist
- Division of Cancer Prevention and Population Sciences, Department of Heath Disparities Research, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Pablo C Okhuysen
- Department of Infectious Diseases, Infection Control, and Employee Health, Division of Internal Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Samir M Hanash
- Red & Charline McCombs Institute for the Early Detection and Treatment of Cancer, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Division of Cancer Prevention and Population Sciences, Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Joseph F Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Paul Scheet
- Division of Cancer Prevention and Population Sciences, Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Carrie R Daniel
- Division of Cancer Prevention and Population Sciences, Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| |
Collapse
|
5
|
Kain BN, Tran BT, Luna PN, Cao R, Le DT, Florez MA, Maneix L, Toups JD, Morales-Mantilla DE, Koh S, Han H, Jaksik R, Huang Y, Catic A, Shaw CA, King KY. Hematopoietic stem and progenitor cells confer cross-protective trained immunity in mouse models. iScience 2023; 26:107596. [PMID: 37664586 PMCID: PMC10470378 DOI: 10.1016/j.isci.2023.107596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 07/24/2023] [Accepted: 08/07/2023] [Indexed: 09/05/2023] Open
Abstract
Recent studies suggest that infection reprograms hematopoietic stem and progenitor cells (HSPCs) to enhance innate immune responses upon secondary infectious challenge, a process called "trained immunity." However, the specificity and cell types responsible for this response remain poorly defined. We established a model of trained immunity in mice in response to Mycobacterium avium infection. scRNA-seq analysis revealed that HSPCs activate interferon gamma-response genes heterogeneously upon primary challenge, while rare cell populations expand. Macrophages derived from trained HSPCs demonstrated enhanced bacterial killing and metabolism, and a single dose of recombinant interferon gamma exposure was sufficient to induce similar training. Mice transplanted with influenza-trained HSPCs displayed enhanced immunity against M. avium challenge and vice versa, demonstrating cross protection against antigenically distinct pathogens. Together, these results indicate that heterogeneous responses to infection by HSPCs can lead to long-term production of bone marrow derived macrophages with enhanced function and confer cross-protection against alternative pathogens.
Collapse
Affiliation(s)
- Bailee N. Kain
- Graduate Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, TX, USA
- Department of Pediatrics – Division of Infectious Disease, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
| | - Brandon T. Tran
- Department of Pediatrics – Division of Infectious Disease, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Graduate Program in Cancer and Cell Biology, Baylor College of Medicine, Houston, TX, USA
| | - Pamela N. Luna
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Ruoqiong Cao
- Department of Pediatrics – Division of Infectious Disease, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX, USA
- Graduate Program in Immunology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Duy T. Le
- Department of Pediatrics – Division of Infectious Disease, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX, USA
- Graduate Program in Immunology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
| | - Marcus A. Florez
- Graduate Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, TX, USA
- Department of Pediatrics – Division of Infectious Disease, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
| | - Laure Maneix
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Jack D. Toups
- Department of Pediatrics – Division of Infectious Disease, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
| | - Daniel E. Morales-Mantilla
- Department of Pediatrics – Division of Infectious Disease, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX, USA
- Graduate Program in Immunology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
| | - Scott Koh
- Department of Pediatrics – Division of Infectious Disease, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX, USA
| | - Hyojeong Han
- Department of Pediatrics – Division of Hematology Oncology, Baylor College of Medicine, Houston, TX, USA
| | - Roman Jaksik
- Department of Systems Biology and Engineering and Biotechnology Centre, Silesian University of Technology, 44-100 Gliwice, Poland
| | - Yun Huang
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M Health, Houston, TX, USA
| | - Andre Catic
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Chad A. Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Katherine Y. King
- Graduate Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, TX, USA
- Department of Pediatrics – Division of Infectious Disease, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX, USA
- Graduate Program in Immunology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
| |
Collapse
|
6
|
Belanger Deloge R, Zhao X, Luna PN, Shaw CA, Rosenfeld JA, Scott DA. High molecular diagnostic yields and novel phenotypic expansions involving syndromic anorectal malformations. Eur J Hum Genet 2023; 31:296-303. [PMID: 36474027 PMCID: PMC9995493 DOI: 10.1038/s41431-022-01255-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 11/04/2022] [Accepted: 11/22/2022] [Indexed: 12/12/2022] Open
Abstract
Evidence suggests that genetic factors contribute to the development of anorectal malformations (ARMs). However, the etiology of the majority of ARMs cases remains unclear. Exome sequencing (ES) may be underutilized in the diagnostic workup of ARMs due to uncertainty regarding its diagnostic yield. In a clinical database of ~17,000 individuals referred for ES, we identified 130 individuals with syndromic ARMs. A definitive or probable diagnosis was made in 45 of these individuals for a diagnostic yield of 34.6% (45/130). The molecular diagnostic yield of individuals who initially met criteria for VACTERL association was lower than those who did not (26.8% vs 44.1%; p = 0.0437), suggesting that non-genetic factors may play an important role in this subset of syndromic ARM cases. Within this cohort, we identified two individuals who carried de novo pathogenic frameshift variants in ADNP, two individuals who were homozygous for pathogenic variants in BBS1, and single individuals who carried pathogenic or likely pathogenic variants in CREBBP, EP300, FANCC, KDM6A, SETD2, and SMARCA4. The association of these genes with ARMs was supported by previously published cases, and their similarity to known ARM genes as demonstrated using a machine learning algorithm. These data suggest that ES should be considered for all individuals with syndromic ARMs in whom a molecular diagnosis has not been made, and that ARMs represent a low penetrance phenotype associated with Helsmoortel-van der Aa syndrome, Bardet-Biedl syndrome 1, Rubinstein-Taybi syndromes 1 and 2, Fanconi anemia group C, Kabuki syndrome 2, SETD2-related disorders, and Coffin-Siris syndrome 4.
Collapse
Affiliation(s)
- Raymond Belanger Deloge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Xiaonan Zhao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Baylor Genetics, Houston, TX, USA
| | - Pamela N Luna
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Chad A Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Daryl A Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA.
| |
Collapse
|
7
|
Sy MR, Chauhan J, Prescott K, Imam A, Kraus A, Beleza A, Salkeld L, Hosdurga S, Parker M, Vasudevan P, Islam L, Goel H, Bain N, Park SM, Mohammed S, Dieterich K, Coutton C, Satre V, Vieville G, Donaldson A, Beneteau C, Ghoumid J, Bogaert KVD, Boogaerts A, Boudry E, Vanlerberghe C, Petit F, Bernardini L, Torres B, Mattina T, Carli D, Mandrile G, Pinelli M, Brunetti-Pierri N, Neas K, Beddow R, Tørring PM, Faletra F, Spedicati B, Gasparini P, Mussa A, Ferrero GB, Lampe A, Lam W, Bi W, Bacino CA, Kuwahara A, Bush JO, Zhao X, Luna PN, Shaw CA, Rosenfeld JA, Scott DA. Exome sequencing efficacy and phenotypic expansions involving esophageal atresia/tracheoesophageal fistula plus. Am J Med Genet A 2022; 188:3492-3504. [PMID: 36135330 PMCID: PMC9669235 DOI: 10.1002/ajmg.a.62976] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/01/2022] [Accepted: 09/05/2022] [Indexed: 01/31/2023]
Abstract
Esophageal atresia/tracheoesophageal fistula (EA/TEF) is a life-threatening birth defect that often occurs with other major birth defects (EA/TEF+). Despite advances in genetic testing, a molecular diagnosis can only be made in a minority of EA/TEF+ cases. Here, we analyzed clinical exome sequencing data and data from the DECIPHER database to determine the efficacy of exome sequencing in cases of EA/TEF+ and to identify phenotypic expansions involving EA/TEF. Among 67 individuals with EA/TEF+ referred for clinical exome sequencing, a definitive or probable diagnosis was made in 11 cases for an efficacy rate of 16% (11/67). This efficacy rate is significantly lower than that reported for other major birth defects, suggesting that polygenic, multifactorial, epigenetic, and/or environmental factors may play a particularly important role in EA/TEF pathogenesis. Our cohort included individuals with pathogenic or likely pathogenic variants that affect TCF4 and its downstream target NRXN1, and FANCA, FANCB, and FANCC, which are associated with Fanconi anemia. These cases, previously published case reports, and comparisons to other EA/TEF genes made using a machine learning algorithm, provide evidence in support of a potential pathogenic role for these genes in the development of EA/TEF.
Collapse
Affiliation(s)
- Mary R. Sy
- Department of Molecular and Human Genetics, Baylor College
of Medicine, Houston, TX, USA
| | - Jaynee Chauhan
- Yorkshire Regional Genetics Service, Leeds Teaching
Hospitals NHS Trust, Chapel Allerton Hospital, Leeds, UK
| | - Katrina Prescott
- Yorkshire Regional Genetics Service, Leeds Teaching
Hospitals NHS Trust, Chapel Allerton Hospital, Leeds, UK
| | - Aliza Imam
- Yorkshire Regional Genetics Service, Leeds Teaching
Hospitals NHS Trust, Chapel Allerton Hospital, Leeds, UK
| | - Alison Kraus
- Yorkshire Regional Genetics Service, Leeds Teaching
Hospitals NHS Trust, Chapel Allerton Hospital, Leeds, UK
| | - Ana Beleza
- Clinical Genetics Department, University Hospitals Bristol
and Weston, Bristol NHS Foundation, Bristol, UK
| | - Lee Salkeld
- Whiteladies Medical Group, Whatley Road, Clifton, Bristol,
UK
| | - Saraswati Hosdurga
- Community Children’s Health Partnership, Sirona
Health and Care, Bristol, UK
| | - Michael Parker
- Sheffield Children’s NHS Foundation Trust,
Sheffield, UK
| | | | - Lily Islam
- Birmingham Women’s and Children’s Hospital
NHS Foundation Trust, Birmingham, UK
| | - Himanshu Goel
- Hunter New England Local Health District, Hunter Genetics,
Waratah, NSW, Australia
- University of Newcastle, Callaghan, NSW, Australia
| | - Nicole Bain
- Department of Molecular Medicine, New South Wales Health
Pathology, Newcastle, Australia
| | - Soo-Mi Park
- East Anglian Medical Genetics Service, Cambridge
University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | - Klaus Dieterich
- Département de Génétique et
Procréation, Hôpital Couple Enfant, CHU Grenoble, Grenoble Cedex,
France
- INSERM U1216 Grenoble Institut des Neurosciences,
Cellular Myology and Pathology, Grenoble, France
| | - Charles Coutton
- Département de Génétique et
Procréation, Hôpital Couple Enfant, CHU Grenoble, Grenoble Cedex,
France
- Genetic Epigenetic and Therapies of Infertility team,
Institute for Advanced Biosciences, Inserm U 1209, CNRS UMR 5309, Université
Grenoble Alpes, Grenoble, France
| | - Véronique Satre
- Département de Génétique et
Procréation, Hôpital Couple Enfant, CHU Grenoble, Grenoble Cedex,
France
- Genetic Epigenetic and Therapies of Infertility team,
Institute for Advanced Biosciences, Inserm U 1209, CNRS UMR 5309, Université
Grenoble Alpes, Grenoble, France
| | - Gaëlle Vieville
- Département de Génétique et
Procréation, Hôpital Couple Enfant, CHU Grenoble, Grenoble Cedex,
France
| | - Alan Donaldson
- Clinical Genetics Department, St Michaels Hospital,
Bristol, UK
| | - Claire Beneteau
- Nantes Université, CHU de Nantes, UF 9321 de
Fœtopathologie et Génétique, Nantes, France
| | - Jamal Ghoumid
- Université de Lille, ULR7364 RADEME, CHU Lille,
Clinique de Génétique Guy Fontaine, Lille, France
| | - Kris Van Den Bogaert
- Center for Human Genetics, University Hospitals
Leuven–KU Leuven, Leuven, Belgium
| | - Anneleen Boogaerts
- Center for Human Genetics, University Hospitals
Leuven–KU Leuven, Leuven, Belgium
| | - Elise Boudry
- CHU Lille, Institut de Génétique
Médicale, Lille, France
| | - Clémence Vanlerberghe
- Université de Lille, ULR7364 RADEME, CHU Lille,
Clinique de Génétique Guy Fontaine, Lille, France
| | - Florence Petit
- Université de Lille, ULR7364 RADEME, CHU Lille,
Clinique de Génétique Guy Fontaine, Lille, France
| | - Laura Bernardini
- Medical Genetics Unit, Fondazione IRCCS Casa Sollievo
della Sofferenza, San Giovanni Rotondo, Italy
| | - Barbara Torres
- Medical Genetics Unit, Fondazione IRCCS Casa Sollievo
della Sofferenza, San Giovanni Rotondo, Italy
| | - Teresa Mattina
- Department of Biomedical and Biotechnological Sciences,
Medical Genetics, University of Catania, Catania, Italy
- Scientific Foundation and Clinic G. B. Morgagni,
Catania, Italy
| | - Diana Carli
- Department of Public Health and Pediatrics, University
of Torino, Torino, Italy
| | - Giorgia Mandrile
- Medical Genetics Unit, San Luigi University Hospital,
University of Torino, Orbassano, Italy
| | - Michele Pinelli
- Department of Molecular Medicine and Medical
Biotechnology, University of Naples Federico II, Naples, Italy
- Telethon Institute of Genetics and Medicine (TIGEM),
Pozzuoli, Italy
| | - Nicola Brunetti-Pierri
- Telethon Institute of Genetics and Medicine (TIGEM),
Pozzuoli, Italy
- Department of Translational Medicine, University of
Naples Federico II, Naples, Italy
| | | | - Rachel Beddow
- Wellington Regional Genetics laboratory, Wellington, New
Zealand
| | - Pernille M. Tørring
- Department of Clinical Genetics, Odense University
Hospital, Odense C, Denmark
| | - Flavio Faletra
- Institute for Maternal and Child Health - IRCCS Burlo
Garofolo, Trieste, Italy
| | - Beatrice Spedicati
- Department of Medicine, Surgery and Health Sciences,
University of Trieste, Trieste, Italy
| | - Paolo Gasparini
- Institute for Maternal and Child Health - IRCCS Burlo
Garofolo, Trieste, Italy
- Department of Medicine, Surgery and Health Sciences,
University of Trieste, Trieste, Italy
| | - Alessandro Mussa
- Department of Public Health and Pediatrics, University
of Torino, Torino, Italy
- Pediatric Clinical Genetics Unit, Regina Margherita
Childrens Hospital, Torino, Italy
| | | | - Anne Lampe
- South East Scotland Clinical Genetics Service, Western
General Hospital, Edinburgh, UK
| | - Wayne Lam
- Department of Clinical Genetics, Western General
Hospital, Edinburgh, UK
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College
of Medicine, Houston, TX, USA
- Baylor Genetics, Houston, TX, 77021, USA
| | - Carlos A. Bacino
- Department of Molecular and Human Genetics, Baylor College
of Medicine, Houston, TX, USA
| | - Akela Kuwahara
- Department of Cell and Tissue Biology, University of
California San Francisco, San Francisco, USA
- Institute for Human Genetics, University of California
San Francisco, San Francisco, USA
- Eli and Edythe Broad Center of Regeneration Medicine and
Stem Cell Research, University of California San Francisco, San Francisco, USA
| | - Jeffrey O. Bush
- Department of Cell and Tissue Biology, University of
California San Francisco, San Francisco, USA
- Institute for Human Genetics, University of California
San Francisco, San Francisco, USA
- Eli and Edythe Broad Center of Regeneration Medicine and
Stem Cell Research, University of California San Francisco, San Francisco, USA
| | - Xiaonan Zhao
- Department of Molecular and Human Genetics, Baylor College
of Medicine, Houston, TX, USA
- Baylor Genetics, Houston, TX, 77021, USA
| | - Pamela N. Luna
- Department of Molecular and Human Genetics, Baylor College
of Medicine, Houston, TX, USA
| | - Chad A. Shaw
- Department of Molecular and Human Genetics, Baylor College
of Medicine, Houston, TX, USA
| | - Jill A. Rosenfeld
- Department of Molecular and Human Genetics, Baylor College
of Medicine, Houston, TX, USA
| | - Daryl A. Scott
- Department of Molecular and Human Genetics, Baylor College
of Medicine, Houston, TX, USA
- Department of Molecular Physiology and Biophysics,
Baylor College of Medicine, Houston, TX, USA
| |
Collapse
|
8
|
Kumar RD, Burns BA, Vandeventer PJ, Luna PN, Shaw CA. Selection for or against escape from nonsense mediated decay is a novel signature for the detection of cancer genes. Cancer Genet 2021; 258-259:80-84. [PMID: 34592632 DOI: 10.1016/j.cancergen.2021.09.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 08/18/2021] [Accepted: 09/20/2021] [Indexed: 01/02/2023]
Abstract
Escape from nonsense mediated mRNA decay (NMD-) can produce activated or inactivated gene products, and bias in rates of escape can identify functionally important genes in germline disease. We hypothesized that the same would be true of cancer genes, and tested for NMD- bias within The Cancer Genome Atlas pan-cancer somatic mutation dataset. We identify 29 genes that show significantly elevated or suppressed rates of NMD-. This novel approach to cancer gene discovery reveals genes not previously cataloged as potentially tumorigenic, and identifies many potential driver mutations in known cancer genes for functional characterization.
Collapse
Affiliation(s)
- Runjun D Kumar
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS225, Houston, TX 77030, United States
| | - Briana A Burns
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS225, Houston, TX 77030, United States
| | - Paul J Vandeventer
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS225, Houston, TX 77030, United States
| | - Pamela N Luna
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS225, Houston, TX 77030, United States
| | - Chad A Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS225, Houston, TX 77030, United States; Baylor Genetics, Houston, TX, United States; Department of Statistics, Rice University, Houston, TX, United States.
| |
Collapse
|
9
|
Luna PN, Mansbach JM, Shaw CA. A joint modeling approach for longitudinal microbiome data improves ability to detect microbiome associations with disease. PLoS Comput Biol 2020; 16:e1008473. [PMID: 33315858 PMCID: PMC7769610 DOI: 10.1371/journal.pcbi.1008473] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 12/28/2020] [Accepted: 10/27/2020] [Indexed: 02/02/2023] Open
Abstract
Changes in the composition of the microbiome over time are associated with myriad human illnesses. Unfortunately, the lack of analytic techniques has hindered researchers' ability to quantify the association between longitudinal microbial composition and time-to-event outcomes. Prior methodological work developed the joint model for longitudinal and time-to-event data to incorporate time-dependent biomarker covariates into the hazard regression approach to disease outcomes. The original implementation of this joint modeling approach employed a linear mixed effects model to represent the time-dependent covariates. However, when the distribution of the time-dependent covariate is non-Gaussian, as is the case with microbial abundances, researchers require different statistical methodology. We present a joint modeling framework that uses a negative binomial mixed effects model to determine longitudinal taxon abundances. We incorporate these modeled microbial abundances into a hazard function with a parameterization that not only accounts for the proportional nature of microbiome data, but also generates biologically interpretable results. Herein we demonstrate the performance improvements of our approach over existing alternatives via simulation as well as a previously published longitudinal dataset studying the microbiome during pregnancy. The results demonstrate that our joint modeling framework for longitudinal microbiome count data provides a powerful methodology to uncover associations between changes in microbial abundances over time and the onset of disease. This method offers the potential to equip researchers with a deeper understanding of the associations between longitudinal microbial composition changes and disease outcomes. This new approach could potentially lead to new diagnostic biomarkers or inform clinical interventions to help prevent or treat disease.
Collapse
Affiliation(s)
- Pamela N. Luna
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Statistics, Rice University, Houston, Texas, United States of America
| | - Jonathan M. Mansbach
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Chad A. Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Statistics, Rice University, Houston, Texas, United States of America
| |
Collapse
|
10
|
Mansbach JM, Luna PN, Shaw CA, Hasegawa K, Petrosino JF, Piedra PA, Sullivan AF, Espinola JA, Stewart CJ, Camargo CA. Increased Moraxella and Streptococcus species abundance after severe bronchiolitis is associated with recurrent wheezing. J Allergy Clin Immunol 2020; 145:518-527.e8. [PMID: 31738994 PMCID: PMC7010548 DOI: 10.1016/j.jaci.2019.10.034] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 09/16/2019] [Accepted: 10/23/2019] [Indexed: 01/22/2023]
Abstract
BACKGROUND The role of the airway microbiome in the development of recurrent wheezing and asthma remains uncertain, particularly in the high-risk group of infants hospitalized for bronchiolitis. OBJECTIVE We sought to examine the relation of the nasal microbiota at bronchiolitis-related hospitalization and 3 later points to the risk of recurrent wheezing by age 3 years. METHODS In 17 US centers researchers collected clinical data and nasal swabs from infants hospitalized for bronchiolitis. Trained parents collected nasal swabs 3 weeks after hospitalization and, when healthy, during the summer and 1 year after hospitalization. We applied 16S rRNA gene sequencing to all nasal swabs. We used joint modeling to examine the relation of longitudinal nasal microbiota abundances to the risk of recurrent wheezing. RESULTS Among 842 infants hospitalized for bronchiolitis, there was 88% follow-up at 3 years, and 31% had recurrent wheezing. The median age at enrollment was 3.2 months (interquartile range, 1.7-5.8 months). In joint modeling analyses adjusting for 16 covariates, including viral cause, a 10% increase in relative abundance of Moraxella or Streptococcus species 3 weeks after day 1 of hospitalization was associated with an increased risk of recurrent wheezing (hazard ratio [HR] of 1.38 and 95% high-density interval [HDI] of 1.11-1.85 and HR of 1.76 and 95% HDI of 1.13-3.19, respectively). Increased Streptococcus species abundance the summer after hospitalization was also associated with a greater risk of recurrent wheezing (HR, 1.76; 95% HDI, 1.15-3.27). CONCLUSIONS Enrichment of Moraxella or Streptococcus species after bronchiolitis hospitalization was associated with recurrent wheezing by age 3 years, possibly providing new avenues to ameliorate the long-term respiratory outcomes of infants with severe bronchiolitis.
Collapse
Affiliation(s)
- Jonathan M Mansbach
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Mass.
| | - Pamela N Luna
- Department of Statistics, Rice University, Houston, Tex
| | - Chad A Shaw
- Department of Statistics, Rice University, Houston, Tex; Department of Molecular and Human Genetics, Baylor University, Houston, Tex
| | - Kohei Hasegawa
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Mass
| | - Joseph F Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, Tex
| | - Pedro A Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, Houston, Tex
| | - Ashley F Sullivan
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Mass
| | - Janice A Espinola
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Mass
| | - Christopher J Stewart
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, Tex; Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Carlos A Camargo
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Mass
| |
Collapse
|
11
|
Luna PN, Hasegawa K, Ajami NJ, Espinola JA, Henke DM, Petrosino JF, Piedra PA, Sullivan AF, Camargo CA, Shaw CA, Mansbach JM. The association between anterior nares and nasopharyngeal microbiota in infants hospitalized for bronchiolitis. Microbiome 2018; 6:2. [PMID: 29298732 PMCID: PMC5751828 DOI: 10.1186/s40168-017-0385-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Accepted: 12/14/2017] [Indexed: 05/09/2023]
Abstract
BACKGROUND The airway microbiome is a subject of great interest for the study of respiratory disease. Anterior nare samples are more accessible than samples from deeper within the nasopharynx. However, the correlation between the microbiota found in the anterior nares and the microbiota found within the nasopharynx is unknown. We assessed the anterior nares and nasopharyngeal microbiota to determine (1) the relation of the microbiota from these two upper airway sites and (2) if associations were maintained between the microbiota from these two sites and two bronchiolitis severity outcomes. RESULTS Among 815 infants hospitalized at 17 US centers for bronchiolitis with optimal 16S rRNA gene sequence reads from both nasal swab and nasopharyngeal aspirate samples, there were strong intra-individual correlations in the microbial communities between the two sample types, especially relating to Haemophilus and Moraxella genera. By contrast, we found a high abundance of Staphylococcus genus in the nasal swabs-a pattern not found in the nasopharyngeal samples and not informative when predicting the dominant nasopharyngeal genera. While these disparities may have been due to sample processing differences (i.e., nasal swabs were mailed at ambient temperature to emulate processing of future parent collected swabs while nasopharyngeal aspirates were mailed on dry ice), a previously reported association between Haemophilus-dominant nasopharyngeal microbiota and the increased severity of bronchiolitis was replicated utilizing the nasal swab microbiota and the same outcome measures: intensive care use (adjusted OR 6.43; 95% CI 2.25-20.51; P < 0.001) and hospital length-of-stay (adjusted OR 4.31; 95% CI, 1.73-11.11; P = 0.002). Additionally, Moraxella-dominant nasopharyngeal microbiota was previously identified as protective against intensive care use, a result that was replicated when analyzing the nasal swab microbiota (adjusted OR 0.30; 95% CI, 0.11-0.64; P = 0.01). CONCLUSIONS While the microbiota of the anterior nares and the nasopharynx are distinct, there is considerable overlap between the bacterial community compositions from these two anatomic sites. Despite processing differences between the samples, these results indicate that microbiota severity associations from the nasopharynx are recapitulated in the anterior nares, suggesting that nasal swab samples not only are effective sample types, but also can be used to detect microbial risk markers.
Collapse
Affiliation(s)
- Pamela N Luna
- Department of Statistics, Rice University, Houston, TX, USA
| | - Kohei Hasegawa
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Nadim J Ajami
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Janice A Espinola
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - David M Henke
- Department of Molecular and Human Genetics MS 225, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Joseph F Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Pedro A Piedra
- Department of Molecular Virology and Microbiology and Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Ashley F Sullivan
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Carlos A Camargo
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Chad A Shaw
- Department of Statistics, Rice University, Houston, TX, USA.
- Department of Molecular and Human Genetics MS 225, Baylor College of Medicine, Houston, TX, 77030, USA.
| | | |
Collapse
|
12
|
Stewart CJ, Embleton ND, Clements E, Luna PN, Smith DP, Fofanova TY, Nelson A, Taylor G, Orr CH, Petrosino JF, Berrington JE, Cummings SP. Cesarean or Vaginal Birth Does Not Impact the Longitudinal Development of the Gut Microbiome in a Cohort of Exclusively Preterm Infants. Front Microbiol 2017. [PMID: 28634475 PMCID: PMC5459931 DOI: 10.3389/fmicb.2017.01008] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The short and long-term impact of birth mode on the developing gut microbiome in neonates has potential implications for the health of infants. In term infants, the microbiome immediately following birth across multiple body sites corresponds to birth mode, with increased Bacteroides in vaginally delivered infants. We aimed to determine the impact of birth mode of the preterm gut microbiome over the first 100 days of life and following neonatal intensive care unit (NICU) discharge. In total, 867 stool samples from 46 preterm infants (21 cesarean and 25 vaginal), median gestational age 27 weeks, were sequenced (V4 region 16S rRNA gene, Illumina MiSeq). Of these, 776 samples passed quality filtering and were included in the analysis. The overall longitudinal alpha-diversity and within infant beta-diversity was comparable between cesarean and vaginally delivered infants. Vaginally delivered infants kept significantly more OTUs from 2 months of life and following NICU discharge, but OTUs lost, gained, and regained were not different based on birth mode. Furthermore, the temporal progression of dominant genera was comparable between birth modes and no significant difference was found for any genera following adjustment for covariates. Lastly, preterm gut community types (PGCTs) showed some moderate differences in very early life, but progressed toward a comparable pattern by week 5. No PGCT was significantly associated with cesarean or vaginal birth. Unlike term infants, birth mode was not significantly associated with changes in microbial diversity, composition, specific taxa, or overall microbial development in preterm infants. This may result from the dominating effects of NICU exposures including the universal use of antibiotics immediately following birth and/or the lack of Bacteroides colonizing preterm infants.
Collapse
Affiliation(s)
- Christopher J Stewart
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, HoustonTX, United States
| | - Nicholas D Embleton
- Newcastle Neonatal ServiceRoyal Victoria Infirmary, Newcastle upon Tyne, United Kingdom
| | - Elizabeth Clements
- School of Science and Engineering, Teesside UniversityMiddlesbrough, United Kingdom
| | - Pamela N Luna
- Department of Statistics, Rice University, HoustonTX, United States
| | - Daniel P Smith
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, HoustonTX, United States
| | - Tatiana Y Fofanova
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, HoustonTX, United States
| | - Andrew Nelson
- Faculty of Health and Life Sciences, Northumbria UniversityNewcastle upon Tyne, United Kingdom
| | - Gillian Taylor
- School of Science and Engineering, Teesside UniversityMiddlesbrough, United Kingdom
| | - Caroline H Orr
- School of Science and Engineering, Teesside UniversityMiddlesbrough, United Kingdom
| | - Joseph F Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, HoustonTX, United States
| | - Janet E Berrington
- Newcastle Neonatal ServiceRoyal Victoria Infirmary, Newcastle upon Tyne, United Kingdom
| | - Stephen P Cummings
- School of Science and Engineering, Teesside UniversityMiddlesbrough, United Kingdom
| |
Collapse
|
13
|
Stewart CJ, Embleton ND, Clements E, Luna PN, Smith DP, Fofanova TY, Nelson A, Taylor G, Orr CH, Petrosino JF, Berrington JE, Cummings SP. Cesarean or Vaginal Birth Does Not Impact the Longitudinal Development of the Gut Microbiome in a Cohort of Exclusively Preterm Infants. Front Microbiol 2017. [PMID: 28634475 DOI: 10.3389/fmicb.2017.01008/full] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023] Open
Abstract
The short and long-term impact of birth mode on the developing gut microbiome in neonates has potential implications for the health of infants. In term infants, the microbiome immediately following birth across multiple body sites corresponds to birth mode, with increased Bacteroides in vaginally delivered infants. We aimed to determine the impact of birth mode of the preterm gut microbiome over the first 100 days of life and following neonatal intensive care unit (NICU) discharge. In total, 867 stool samples from 46 preterm infants (21 cesarean and 25 vaginal), median gestational age 27 weeks, were sequenced (V4 region 16S rRNA gene, Illumina MiSeq). Of these, 776 samples passed quality filtering and were included in the analysis. The overall longitudinal alpha-diversity and within infant beta-diversity was comparable between cesarean and vaginally delivered infants. Vaginally delivered infants kept significantly more OTUs from 2 months of life and following NICU discharge, but OTUs lost, gained, and regained were not different based on birth mode. Furthermore, the temporal progression of dominant genera was comparable between birth modes and no significant difference was found for any genera following adjustment for covariates. Lastly, preterm gut community types (PGCTs) showed some moderate differences in very early life, but progressed toward a comparable pattern by week 5. No PGCT was significantly associated with cesarean or vaginal birth. Unlike term infants, birth mode was not significantly associated with changes in microbial diversity, composition, specific taxa, or overall microbial development in preterm infants. This may result from the dominating effects of NICU exposures including the universal use of antibiotics immediately following birth and/or the lack of Bacteroides colonizing preterm infants.
Collapse
Affiliation(s)
- Christopher J Stewart
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, HoustonTX, United States
| | - Nicholas D Embleton
- Newcastle Neonatal ServiceRoyal Victoria Infirmary, Newcastle upon Tyne, United Kingdom
| | - Elizabeth Clements
- School of Science and Engineering, Teesside UniversityMiddlesbrough, United Kingdom
| | - Pamela N Luna
- Department of Statistics, Rice University, HoustonTX, United States
| | - Daniel P Smith
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, HoustonTX, United States
| | - Tatiana Y Fofanova
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, HoustonTX, United States
| | - Andrew Nelson
- Faculty of Health and Life Sciences, Northumbria UniversityNewcastle upon Tyne, United Kingdom
| | - Gillian Taylor
- School of Science and Engineering, Teesside UniversityMiddlesbrough, United Kingdom
| | - Caroline H Orr
- School of Science and Engineering, Teesside UniversityMiddlesbrough, United Kingdom
| | - Joseph F Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, HoustonTX, United States
| | - Janet E Berrington
- Newcastle Neonatal ServiceRoyal Victoria Infirmary, Newcastle upon Tyne, United Kingdom
| | - Stephen P Cummings
- School of Science and Engineering, Teesside UniversityMiddlesbrough, United Kingdom
| |
Collapse
|